What happens if I discharge my 2nd loan in bankrupcy and continue to pay the primary?

You are still subject to Bankrupcy credit guidelines

This is probably a better question for a bankruptcy expert. From my understanding, the second mortgage would still be a lien on the property, so you would still have to deal with it at some point if you wanted to remain in the home long term, even if you didn't reaffirm during the bankruptcy process. From a credit and lending standpoint, a bankruptcy is a bankruptcy.

As long as you do not sell, you should be fine. The 2nd still has a security interest, so they may want to get paid if you sell at a profit.